Best Science Fiction of the 21st Century?

I'm more of fantasy reader than scifi reader. But I like to read good science fiction (along with mystery, literature, various non-fiction). Because I don't read enough to determine the best of the best I have in the past relied on “generally accepted” lists. Reading Hugo winning novels has been rewarding to this end. However, lately, I feel like the best science fiction is getting over looked. Either that or there has not been much great science fiction lately. Great is defined as books that will be on your “best of” lists 20 years from now.

The Hugo awards are still a good source of good reading but they may have jumped the shark somewhat. I can point to 2001 when a Harry Potter book won.
2002 American Gods – Great book but fantasy
2003 Hominids – Very good (that’s 1)
2004 Paladin of Souls – Very good fantasy
2005 Jonathan Strange – Great but fantasy
2006 Spin Very Good (2)
2007 Rainbows End – I loved his earlier work – this one not so much
2008 Yiddish Policemens Union – Very good, glad I read it but I am not big on alt history
2009 The Graveyard Book - Very good, glad I read it but I am not big on YA
2010 Windup Girl & The City Great (3 or is it 4)
2011 – Blackout – By the time an author wins 3 they seem to be winning on popularity and the qulity does not seem up to par.
2012 - Very good fantasy

That’s 3 for 12 (starting 2001). I know it is a speculative fiction award but the trophy is a rocket. Where is the great science fiction?

What am I looking for? Good question. Post on this site are generally all over the place (or skewed but author input). I would not trust any reviews on Amazon.

So two questions:
Has there been great science fiction written in the 21st century?
Are there credible scifi only awards and year end lists?

Here's one... I'd put Blindsight by Peter Watts high on the list of my great science fiction novels written in the 21st Century. It was a 2007 Hugo, Campbell and Locus nominee. Recall being quite disappointed that it didn't win.

Perhaps the most credible sf award is the Arthur C Clarke Award. The Hugo hasn't picked a decent book as winner for years. The Nebulas are a joke - Jack McDevitt gets shortlisted every year, I think it's in the charter. The BSFA Award has picked some good shortlists and winners in its time, but it too is a popularity context like the Hugo. The Tiptree picks some interesting books most years, and the PKD does occasionally.

Great sf novels of the 21st century...

Omega, Christopher Evans (2008), is very, very good.Light, Nova Swing and Empty Space, My John Harrison (2002 - 2012), are excellent.Life, Gwyneth Jones (2004), is superb.Intrusion, Ken MacLeod (2012), is perhaps his best yet.2312, Kim Stanley Robinson (2012), may also be his best since the Mars trilogy.The Caryatids, Bruce Sterling (2009), definitely needs to be better known than it is.
The Marq'ssan Cycle, L Timmel Duchamp (2005 - 2008), should also be more widely read.

There has been some great SF this century. You can look at the locus recommended reading lists for each year for an overview of part of the books each year, they likely miss some subgenres and not everything will be to everyone's taste but it is a start.

edit: Some great SF (in my opinion), Richard Morgan's Altered Carbon (2002), Charles Stross' Glasshouse (2006) or Halting State (2007), Air by Geoff Ryman (2005), and there are many more the aforementioned Watts amongst them.